Chapter 20: Introduction to Molecular Genetics

Nucleic Acids

made from monomers called nucleotides

what are the 2 major types of nucleic acids?

1) RNA

2) DNA

What 5 nucleotides make up the 2 major types of nucleic acids?

Thymine

Guanine

Cytosine

Adenine

Urical

What does the structure of a nucleotide?

1) Base: nitrogen containing cyclic/heterocyclic base

2) Sugar: Ribose, 5 carbon carbohydrate

3) Phosphoryl groups: 1,23, or 3

What are the 2 different types of bases

1) Purine bases: double ring (A and G)

2) Pyrimidine bases: single ring (C,T, and U)

What are the 2 different forms that that ribose can be?

1) Ribose in RNA (with the OH- group at carbon 2)

2) Deoxyribose in DNA (no OH-group at carbon 2)

What is the difference between a nucleotide and a mucleside?

They both have a base and a ribose, but the nucleosides don’t have the phosphoryl group.

What is the structure of a Nucleic Acid?

1) formed by covalent bonds between the sugar (3’ OH- group and the 5’-phosphoryl group) (phosphoester bond)

What are some features of DNA?

1) Double stranded - 2 polymers of nucleotides

2) complementary strands: same base pairing in interactions

3) DNA needs to form a right-handed double helix

G and C // A and T bond together how?

through specific hydrogen bonding interactions

What is anti-parallel configuration?

double strand reach needs to orient in opposite direction

RNA features compared to DNA

1) Same covalent bonds forming to make the polymer

2) RNA is single-stranded

3) Thymine is replaced with Uracil

4) Ribose have 2’ hydroxyl

What are the three classes of RNA molecules

1) messenger RNA

2) transfer RNA

3) Ribosome RNA

What are chromosomes?

pieces of DNA that contain genetic instructions of an organism

What is a genome?

collection of all genes of a specific organism

What is Prokaryotic Chromosomes?

single chromosome, circular DNA molecule

Features of prokaryotic chromosomes?

\-double stranded

\-antiparallel

\-complementary

\-helical structure

\-supercoiling: helix is coiled to itself

\-protein core: nucleoid

What is Eukaryotic Chromosomes?

\-number and size of the chromosome are highly variable between different organisms.

\-located in the nucleus of each cell structure → made from chromatin = DNA + protein

What are histones?

protein that the DNA double helix “wraps” around

\-octamer of histones (8 proteins)

What are nucleosomes?

DNA strand that is wrapped around the histone octamer.

What is the central dogma of biochemistry?

DNA --→ mRNA --→ protein

what enzyme truns DNA to mRNA?

transcription: RNA polymerase

what enzyme turns mRNA into protein?

translated: ribosome

What enzyme can turn DNA into more DNA?

replication: DNA polymerase

What is DNA replication?

for DNA to be replicated before a cell divides, each new daughter call needs to inherit a copy of each gene.

What is the mechanism of replication?

semiconservative

\-each gene has 2 DNA strands; 1 strand is the parental DNA while also synthesizing new strands from each parental strands

2 main features of the replication process?

\-replication origin

\-replication fork

replication origin

unique nucleotide sequence on the chromosome that signals where replication should begin.

replication fork

where DNA replication is occuring

\-2 forks moving in opposite directions that replicate about 500 nucleotides per second

Important proteins and enzymes in DNA replication?

1) separate the 2 parental (original strands of DNA

\-helicase

\-topoisomerase

\-single-stranded binding proteins

\-primase

2) Synthesize the new daughter strands of DNA

\-Main enzyme: DNA polymerase III

Helicase

enzyme that breaks the hydrogen bonds between base pairs

topoisomerase

gets rid of supercoiling

single-stranded binding proteins

bind to separate single-stranded DNA to keep 2 strands apart

primase

enzyme that synthesizes a “primer” (piece of RNA where new DNA sequence being replication)

DNA polymerase III

synthesize new DNA in the 5’ to 3’ direction by catalyzing formation of new phosphoester bond between a 3’ hydroxyl group and incoming nucleotides 5’ phosphoryl group

What are the 2 types of parental strands.

Leading strand: replicated continuously.

Lagging strand: replicated discontinuously.

Leading strand?

single RNA primer at replication origin, only utilizes DNA polymer III, continuously catalyze addition of nucleotides

Lagging strand?

multiple RNA primers throughout the DNA sequence , 2 DNA polymerases utilized → DNA pol III ( catalyze addition of nucleotides) and DNA pol II (nudrases activity: remove RNA primers)

DNA polymerase II

polymerase activity (fills gaps with appropriate DNA nucleotide)

DNA ligase

enzyme that ligates (or seals) together covalently bond “fragments: of DNA on the lagging strand.

What is the process of transcription

catalyzed by enzyme RNA polymerase and produce mRNA by a copy of 1 DNA strand (turns DNA into mRNA)

5’-ATGCGATAG-3’ convert to antisense

3’-TACGCTATC-5’

3’-TACGCTATC-5’ convert to mRNA

5’-AUGCGAUAG-3’

What are the 3 stages of Transcription?

1) Initiation

2) Elongation

3) Termination

What is initiation?

the promoter region of the DNA that signals RNA polymerase to bind

Elongation?

formation of new phosphoester binds 1 nucleotide added at a time

What is Termination?

Unique DNA sequence that signals stop/release of the RNA polymerase

(prokaryotic cells end here → get the final form of mRNA)

What is the steps of Eukaryotic mRNA processing?

1) Addition of a 5’ cap structure (added to the 5’ nucleotide of the mRNA). required for efficient translation

2) RNA splicing-removal of specific regions of the mRNA that are not protein coding

3) Addition of a poly (A) tail. (about 100 to 200 nucleotides added to the 3’ end of mRNA)

What are exons?

coding region-codons needed for the amino sequence of the protein

What are introns?

noncoding regions that need to be removed via splicing

What is the process of translation?

convert mRNA into a polypeptide (mRNA serves as the template; has codons)

What are the key players in translation?

1) Ribosome- ribonucleopretion complex

2) mRNA

3) tRNA

What does ribosomes do?

1) Small ribosomal subunits: 1 rRNA + 33 protein

2) Large ribosomal subunit: 3rRNA + 49 proteins

3) catalyze formation of peptide bonds between individual amino acids

What does mRNA do?

template that provides codons for specific amino acids

What does tRNA do?

\-delivers specific amino acids to the cite of synthesis

\-contains anticodon loop= complementary to the codon on mRNA

What are the 3 stages that take place in translation?

1) Initiation

2) Elongation

2) Termination

Initiation

\: proteins called initiation factors, mRNA start codon: AUG, initiator tRNA = tRNA for methionine

Elongation steps

1) Aminoacly tRNA bind to the “A” site on the ribosome

2) Peptide bond formation \*catalyzed by peptidyl transferase (ribosome) (occurs in “p” site of the ribosome

3) Translocation of the ribosome down the mRNA to the next codon. Shift new peptide tRNA from a-site to p-site

“Reading Frames”

spaced in codons- 3 different ways “read”